Supporting data for: Effect of changing swarm's fastidious boundary value on environmental DNA clustering results

Supporting material for the publication :

Effect of changing swarm’s fastidious boundary value on environmental DNA clustering results (working title)

by Milena Königshofen and Frédéric Mahé

In this study, Königshofen & Mahé use three published metabarcoding SSU rRNA datasets (18S V4, 18S V9 and 16S V3V4 fasta files) to demonstrate the effect of swarm's fastidious option (https://github.com/torognes/swarm).

Fasta files are derived from publicly available raw fastq files, following the pre-clustering pipeline available at
https://github.com/frederic-mahe/fred-metabarcoding-pipeline

The three original publications are:
- de Vargas et al. (2015): V9 eukaryotic data from the sunlit surface
  layer of the world’s open oceans (doi: 10.1126/science.1261605;
  bioproject: PRJEB6610),
- Mahé et al. (2017): V4 eukaryotic data from surface soils of three
  lowland Neotropical rainforests (doi: 10.1038/s41559-017-0091;
  bioproject: PRJNA317860),
- Alonso et al. (2020): V3V4 bacterial data from plants stems
  collected in Chinese rice terraces (doi: 10.1111/1462-2920.15114;
  bioproject: PRJNA573048).